Installation

The intended use of this pipeline is through the use of a Singularity or Docker image. The image can be built using the Dockerfile found in the repository, or it can be pulled from DockerHub as a singularity using the following command:

singularity pull docker://dcanumn/hbcd_qmri_postproc:<version_num>

Where version_num denotes the specific version of the container. All available versions of the container can be found here.

After downloading the container, singularity is the only other dependency needed for processing. The full usage details can be seen under the Usage section, but the basic command to run the container is as follows:

container_path=/path/to/container.sif
bids_dir=/path/to/bids
output_dir=/path/to/output
qmri_dir=/path/to/qmri
bibsnet_dir=/path/to/bibsnet
singularity run -B $bids_dir:/bids \
 -B $output_dir:/output \
 -B $qmri_dir:/qmri \
 -B $bibsnet_dir:/bibsnet \
 $container_path /data /output participant /qmri /bibsnet

Where “singularity run” is first followed by specific commands for singularity. In this case it is a series of “bind” commands that will give singularity access to the necessary directories needed for processing. This is followed by the path to the container and then the arguments for the primary script to be ran by the container.